While it's certainly possible at someone just complained I would think it would have to be a very important person for the airline to remove the family if the boy was just sitting there quietly.
From what I've read e airline claims the kid was running around. I read a quote that the mom said he was acting no different from a 4-5 year old kid (not sure about this though). If that's the case, I could understand a determination that a large 16 year old acting like a 4-5 year old, particularly if running around, would pose a risk.
Yes, I understand the story says the kid was sitting quietly, very calm, a model citizen, and a frequent flier. But consider the source, a family who has apparently already said they plan on suing.
Yes, airlines need to be cognizant of those with disabilities and doubtless have a long way to go. But is doesn't extend indefinitely. If this was a drunk 26 year old who was acting like a 4-5 year old, running around and causing a scene, removed from the flight despite his friends saying that he would just fall asleep once he gets a snack, would anyone complain?